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I see the error log listed in the process has the wrong name right off the bat. I've tried manually restarting mysql from /etc/init.d, via 'service mysql restart', via restarting the entire server. Nothing seems to get MySQL to read the conf.

Maybe something is breaking when mysqld_safe spins up a mysql instance? No problems reported in the error log when the server starts. Any ideas?

stat("/etc/my.cnf", {st_mode=S_IFREG|0644, st_size=5209, ...}) = 0 open("/etc/my.cnf", O_RDONLY) = 3 (run mysqld directly and the my.cnf is obeyed, as noted in my OP, but when run as a system service it is not using my.cnf)
–
xrefSep 17 '13 at 21:09

whell may be they moved config into /etc/mysql/my.cnf
–
netneladnoSep 17 '13 at 21:19